Contacts of the helix formed by residues 140 - 156 (chain A) in PDB entry 1RIF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 140 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.0 19.5 + - - -
137A THR 4.2 3.7 + - - -
138A SER 2.4 22.6 + - - -
139A ALA* 1.3 68.1 - - - +
141A ARG* 1.3 63.7 + - - +
142A SER* 3.2 8.3 + - - -
143A LEU* 3.3 10.3 + - - +
144A ILE 3.8 1.7 + - - -
180A TYR* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 2.9 34.2 + - + +
136A PRO 3.7 12.4 + - - +
137A THR* 3.3 36.5 + - - +
139A ALA* 3.8 8.5 - - + +
140A GLY* 1.3 73.1 - - - +
142A SER* 1.3 60.4 + - - +
143A LEU 3.2 0.2 - - - -
144A ILE* 3.2 8.9 + - + +
145A GLN* 2.9 32.7 + - - +
232A ASP* 3.1 31.1 + - - +
233A GLU* 2.7 30.5 + - - -
258A LEU* 3.8 29.4 + - + +
259A SER* 4.0 3.8 - - - +
260A GLY* 3.0 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY* 4.5 3.5 + - - -
141A ARG* 1.3 78.8 - - - +
143A LEU* 1.3 55.9 + - - +
145A GLN* 3.5 10.1 + - - +
146A ALA* 2.8 28.9 + - - +
173A MET* 4.4 11.0 - - - -
176A ASP* 3.7 30.7 + - - -
177A PHE* 3.6 6.5 - - - -
180A TYR* 2.5 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.9 35.7 - - + -
112A ILE* 6.0 3.8 - - + -
113A GLU 4.9 1.8 - - - -
114A PRO* 3.7 22.9 - - + -
115A HIS* 5.7 0.2 - - - +
118A GLN* 3.5 26.2 - - - +
140A GLY 3.3 10.0 + - - +
141A ARG 3.2 0.6 - - - -
142A SER* 1.3 78.3 + - - +
144A ILE* 1.3 61.1 + - - +
146A ALA* 4.1 0.2 - - - -
147A LEU* 2.9 48.5 + - + +
180A TYR* 3.6 33.0 - - + +
182A LEU* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.9 31.4 - - + +
121A ALA* 3.9 9.4 - - + -
122A VAL* 3.7 20.6 - - + +
133A LEU* 4.2 15.3 - - + -
135A LEU* 3.4 36.3 - - + -
139A ALA* 4.0 13.7 - - + +
140A GLY 4.2 4.3 - - - +
141A ARG* 3.2 12.9 + - + +
143A LEU* 1.3 78.3 - - - +
145A GLN* 1.3 63.1 + - - +
147A LEU* 3.4 1.3 + - - -
148A LEU* 3.1 37.0 + - + +
258A LEU* 4.3 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG 2.9 24.1 + - - +
142A SER* 3.7 5.6 + - - +
144A ILE* 1.3 78.4 - - + +
146A ALA* 1.3 55.1 + - - +
148A LEU* 3.4 4.7 + - + +
149A ALA* 3.0 30.1 + - - +
162A ILE* 3.8 13.9 - - + +
173A MET* 3.2 31.6 - - - +
177A PHE* 3.8 11.7 - - + -
230A MET* 3.6 30.2 - - - +
232A ASP* 3.5 36.4 - - - +
258A LEU* 3.9 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER 2.8 19.1 + - - +
143A LEU* 3.7 5.2 - - - +
145A GLN* 1.3 76.8 - - - +
147A LEU* 1.3 57.4 + - - +
149A ALA 3.4 0.3 + - - -
150A ARG* 2.9 29.6 + - - +
177A PHE* 3.5 26.9 - - + -
180A TYR* 3.9 16.6 - - + -
182A LEU* 3.8 20.3 - - + +
183A PHE* 3.6 6.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 6.0 0.2 - - + -
99A TRP* 3.4 13.7 - - + -
100A LEU* 4.2 15.0 - - + -
103A LEU* 3.7 30.5 - - + -
105A ILE* 4.1 7.9 - - + -
114A PRO* 4.2 18.6 - - + -
118A GLN* 5.4 3.8 - - + +
119A LYS* 5.8 1.3 - - - -
122A VAL* 3.9 25.1 - - + -
143A LEU* 2.9 37.4 + - + +
144A ILE* 3.8 4.5 - - - +
146A ALA* 1.3 76.5 - - - +
148A LEU* 1.3 57.7 + - - +
150A ARG* 3.5 2.2 - - + +
151A TYR* 3.0 27.4 + - - +
182A LEU* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 3.9 20.8 - - + +
125A GLY* 4.8 1.3 - - - -
126A LEU* 3.5 31.9 - - + +
133A LEU* 4.3 8.7 - - + -
144A ILE* 3.1 38.2 + - + +
145A GLN* 3.6 9.4 - - + +
147A LEU* 1.3 78.0 - - - +
149A ALA* 1.3 60.8 + - - +
151A TYR* 3.5 5.5 + - - +
152A TYR 3.2 17.2 + - - -
228A MET* 3.2 17.0 - - - +
230A MET* 4.2 12.1 - - + -
256A PHE* 3.7 37.2 - - + -
258A LEU* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN 3.0 16.6 + - - +
146A ALA 3.8 1.6 - - - +
148A LEU* 1.3 74.6 - - - +
150A ARG* 1.3 55.3 + - - +
152A TYR* 3.3 2.9 + - - +
153A LEU* 2.8 35.9 + - - +
160A ILE* 3.9 17.2 - - + +
162A ILE* 4.9 0.4 - - + -
177A PHE* 4.1 11.7 - - + -
183A PHE* 3.6 18.8 - - + -
207A VAL* 4.9 1.1 - - + -
228A MET* 4.0 9.9 - - - -
230A MET* 3.8 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TRP* 4.1 10.1 - - + -
102A LYS* 5.0 3.4 - - - +
103A LEU* 4.6 5.9 - - + +
146A ALA 2.9 17.2 + - - +
147A LEU* 3.5 9.2 - - + +
149A ALA* 1.3 74.7 - - - +
151A TYR* 1.3 64.5 + - - +
153A LEU* 3.2 19.7 + - - +
154A GLU* 2.3 74.7 + - - +
181A ARG 5.6 0.8 + - - -
182A LEU* 3.3 54.8 + - + +
183A PHE* 3.4 8.7 - - + -
187A MET* 5.0 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 2.8 29.9 + - - -
90A GLU 5.2 1.6 + - - -
91A LEU* 4.2 31.5 - - + +
96A PHE* 5.4 0.7 - + - -
99A TRP* 3.6 35.8 - + + +
126A LEU* 3.4 44.0 - - + -
147A LEU 3.0 19.1 + - - +
148A LEU 3.6 4.3 - - - +
150A ARG* 1.3 77.0 - - - +
152A TYR* 1.3 66.8 + - + +
154A GLU* 3.3 0.5 + - - +
155A ASN* 2.9 60.2 + - + +
156A TYR* 4.4 6.3 - + - -
254A PHE* 4.6 3.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU 3.2 3.4 + - - +
149A ALA 3.6 6.3 - - - +
151A TYR* 1.3 84.6 - - - +
153A LEU* 1.3 60.4 + - - +
155A ASN 3.1 0.7 + - - -
156A TYR* 2.8 71.3 + + + +
158A GLY* 3.3 41.5 + - - -
159A LYS 4.0 5.6 - - - -
160A ILE* 3.7 18.4 - - + -
227A GLY* 3.1 36.0 - - - -
228A MET* 3.5 27.6 - - + -
253A MET* 5.0 3.6 - - + +
254A PHE* 3.6 25.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ALA 2.8 21.4 + - - +
150A ARG* 3.2 27.6 + - - +
152A TYR* 1.3 79.7 - - - +
154A GLU* 1.3 63.0 + - + +
156A TYR 3.4 13.5 - - - +
158A GLY 5.6 2.2 - - - +
160A ILE* 4.5 6.7 - - + -
183A PHE* 4.1 15.0 - - + -
187A MET* 4.0 18.6 - - + -
206A PRO* 3.5 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TRP* 2.8 29.8 + - - -
102A LYS* 3.2 24.8 + - - -
103A LEU* 4.5 0.2 - - - +
150A ARG* 2.3 58.8 + - - +
151A TYR 3.8 3.6 - - - +
152A TYR 3.2 0.2 - - - -
153A LEU* 1.3 80.7 - - + +
155A ASN* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TRP* 5.3 2.4 - - - +
151A TYR* 2.9 54.5 + - + +
152A TYR 3.1 2.2 + - - -
154A GLU* 1.3 90.6 + - - +
156A TYR* 1.3 87.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 2.6 34.7 + - - -
129A ARG* 4.1 1.7 + - - -
151A TYR* 4.4 3.4 - + - -
152A TYR* 2.8 53.1 + + + +
153A LEU* 3.4 17.2 - - - +
154A GLU 3.8 0.8 - - - -
155A ASN* 1.3 97.1 - - + +
157A GLU* 1.3 65.7 + - - +
158A GLY 3.6 1.5 - - - +
253A MET* 3.5 30.4 - - + -
254A PHE* 3.9 19.5 - + - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il